Rather than two desktops that I can move windows across (full sizing a window only fills one monitor) I have one large desktop split across both screens and centered between the two. Full-sizing a window spans the two monitors.

I'm using nvidia-drivers-173.14.36 and the xinerama use flag is set in make.conf

I'm on a different driver than you (304.94), still nvidia, and I'm getting segmentation faults when shutting down X. I'm still trying to troubleshoot it, but in regard to your question, have you tried creating a new xorg.conf file? I'm also using dual monitors, you can try my layout as a guide.

I just thought I'd chime in and report the same problem of multi-monitor display breaking since the last emerge -avuD world. My driver and xorg.conf is the same as MikeSummers. I am only now starting to investigate and will report back here with any progress I make.

So far I've tried a number of nvidia-xconfig combinations without success, I can't keep the window manager (openbox) from spreading the windows across both monitors or centering tint in the middle of the two.

I decided to try to quick fix the issue until the broken-ness has passed... mask >=xorg-server-1.13. Surprisingly, only the xorg-server itself needed to be re-emerged on a emerge -avuD world (no blocking). I'm a guessin that this might possibly break on re-boot... building right now will report back after re-boot._________________ProDataLab.com -- A Focus On Efficiency

On re-boot, I got the kdm and no input devices worked, so I re-installed 1.13. But, I noticed the emerge messages this time and realized that I should have rebuilt any X11 modules and also that it was recommended to include the 'keymap' use flag for my udev install.. so now I'm going to try the same mask again and see if it works this time without needing to mask all the other newly installed X11 dependencies. ahl b bach ... in a few minutes or so._________________ProDataLab.com -- A Focus On Efficiency